view IDMapper.xml @ 1:17e8c91b70d5 draft

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<?xml version='1.0' encoding='UTF-8'?>
<tool id="IDMapper" name="IDMapper" version="1.12.0">
  <description>Assigns protein/peptide identifications to features or consensus features.</description>
  <macros>
    <token name="@EXECUTABLE@">IDMapper</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>IDMapper

-id ${param_id}
-in ${param_in}
-out ${param_out}
-rt_tolerance ${param_rt_tolerance}
-mz_tolerance ${param_mz_tolerance}
-mz_measure ${param_mz_measure}
-mz_reference ${param_mz_reference}
${param_ignore_charge}
-threads \${GALAXY_SLOTS:-24} 
${param_use_centroid_rt}
${param_use_centroid_mz}
${param_use_subelements}
</command>
  <inputs>
    <param name="param_id" type="data" format="idXML" optional="False" label="Protein/peptide identifications file" help="(-id)"/>
    <param name="param_in" type="data" format="featureXML,consensusXML" optional="False" label="Feature map/consensus map file" help="(-in)"/>
    <param name="param_rt_tolerance" type="float" min="0.0" optional="True" value="5.0" label="RT tolerance (in seconds) for the matching of peptide identifications and (consensus) features.#br#Tolerance is understood as 'plus or minus x', so the matching range increases by twice the given value." help="(-rt_tolerance)"/>
    <param name="param_mz_tolerance" type="float" min="0.0" optional="True" value="20.0" label="m/z tolerance (in ppm or Da) for the matching of peptide identifications and (consensus) features.#br#Tolerance is understood as 'plus or minus x', so the matching range increases by twice the given value." help="(-mz_tolerance)"/>
    <param name="param_mz_measure" type="select" optional="True" value="ppm" label="Unit of 'mz_tolerance'." help="(-mz_measure)">
      <option value="ppm">ppm</option>
      <option value="Da">Da</option>
    </param>
    <param name="param_mz_reference" type="select" optional="True" value="precursor" label="Source of m/z values for peptide identifications. If 'precursor', the precursor-m/z from the idXML is used. If 'peptide',#br#masses are computed from the sequences of peptide hits; in this case, an identification matches if any of its hits matches.#br#('peptide' should be used together with 'feature:use_centroid_mz' to avoid false-positive matches.)" help="(-mz_reference)">
      <option value="precursor">precursor</option>
      <option value="peptide">peptide</option>
    </param>
    <param name="param_ignore_charge" type="boolean" truevalue="-ignore_charge true" falsevalue="-ignore_charge false" checked="false" optional="True" label="For feature/consensus maps: Assign an ID independently of whether its charge state matches that of the (consensus) feature." help="(-ignore_charge)"/>
    <param name="param_use_centroid_rt" type="boolean" truevalue="-feature:use_centroid_rt true" falsevalue="-feature:use_centroid_rt false" checked="false" optional="True" label="Use the RT coordinates of the feature centroids for matching, instead of the RT ranges of the features/mass traces." help="(-use_centroid_rt)"/>
    <param name="param_use_centroid_mz" type="boolean" truevalue="-feature:use_centroid_mz true" falsevalue="-feature:use_centroid_mz false" checked="false" optional="True" label="Use the m/z coordinates of the feature centroids for matching, instead of the m/z ranges of the features/mass traces.#br#(If you choose 'peptide' as 'mz_reference', you should usually set this flag to avoid false-positive matches.)" help="(-use_centroid_mz)"/>
    <param name="param_use_subelements" type="boolean" truevalue="-consensus:use_subelements true" falsevalue="-consensus:use_subelements false" checked="false" optional="True" label="Match using RT and m/z of sub-features instead of consensus RT and m/z. A consensus feature matches if any of its sub-features matches." help="(-use_subelements)"/>
  </inputs>
  <outputs>
    <data name="param_out" label="Output file (the format depends on the input file format)." format="consensusXML">
      <change_format>
        <when input="param_out_type" value="featureXML" format="featureXML"/>
      </change_format>
    </data>
  </outputs>
  <help>**What it does**

Assigns protein/peptide identifications to features or consensus features.


For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_IDMapper.html

@REFERENCES@
</help>
</tool>